comparison base_recalibrator.xml @ 21:6e641ee02851 draft

Fix base_recalibrator.xml option: no_standard_covs

20:3924f62cd4e7

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" />
    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
      <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
      <option value="ReadGroupCovariate" />
      <option value="QualityScoreCovariate" />
      <option value="CycleCovariate" />

21:6e641ee02851

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    <param name="standard_covs" type="boolean" truevalue="" falsevalue="--no_standard_covs" checked="false" label="Do not use the standard set of covariates in addition to the ones selected" help="--no_standard_covs/-noStandard" />
    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
      <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
      <option value="ReadGroupCovariate" />
      <option value="QualityScoreCovariate" />
      <option value="CycleCovariate" />